Zarrify

Convert TIFF/TIFF Stacks, MRC, and N5 files to Zarr (v2) format with OME-NGFF 0.4 metadata.

Prerequisites

You must install Pixi to run this tool.

Install into local env

After you check out the repo, run Pixi to download dependencies and create the local environment:

pixi run dev-install

Usage

Using Configuration Files (Recommended)

Create a YAML configuration file with your conversion parameters:

# config.yaml
src: "/path/to/input/file"
dest: "/path/to/output.zarr"
workers: 100
cluster: "local"  # or "lsf"

# Zarr array configuration
zarr_chunks: [3, 64, 128, 128]
axes: ["c", "z", "y", "x"]
translation: [0.0, 0.0, 0.0, 0.0]
scale: [1.0, 1.0, 0.116, 0.116]
units: ["", "nanometer", "nanometer", "nanometer"]
optimize_reads: true

# Multiscale options (optional)
multiscale: false
ms_workers: 100
data_origin: "raw"  # or "labels"
antialiasing: false
normalize_voxel_size: false
custom_scale_factors : null

# LSF cluster options (if using cluster: "lsf")
log_dir: "/path/to/log/directory"
extra_directives: ["-P myproject"]

Then run:

pixi run zarrify --config config.yaml

You can also override specific config values from the command line:

pixi run zarrify --config config.yaml --workers 200 --scale 1.0 1.0 0.058 0.058

IBM Platform LSF

You can run the pipeline on an LSF cluster by specifying the --cluster=lsf parameter. For example:

export INPUT=/path/to/input
export OUTPUT=/path/to/output.zarr
export LOGDIR=`pwd`
bsub -n 4 -P myproject -o $LOGDIR/jobout.log -e $LOGDIR/joberr.log "/misc/sc/pixi run zarrify --src=$INPUT --dest=$OUTPUT --cluster $CLUSTER --log_dir $LOGDIR/workers --workers 500 --zarr_chunks 3 128 128 128 --extra_directives='-P myproject' --scale 1.0 1.0 0.116 0.116 --optimize_reads"

Python API

Integrating conversion to zarr into the python code

import zarrify
from zarrify.utils.dask_utils import initialize_dask_client

client = initialize_dask_client("local") # or "lsf"
zarrify.to_zarr("input.mrc", "output.zarr", client, workers=20)

Supported formats

• TIFF stacks
• 3D TIFF files
• MRC files
• N5 containers